A computational biologist's personal views on new technologies & publications on genomics & proteomics and their impact on drug discovery

Tuesday, March 23, 2010

What should freshman biology cover?

I've spent some time the last few weeks trying to remember what I learned in freshman biology. Partly this has been triggered by planning for my summer intern (now that I have a specific person lined up for that slot) -- not because of any perceived deficiencies but simply being reminded of the enormous breadth of the biological sciences. It's also no knock on my coursework -- I had a great freshman biology professor (who team-taught with an equally skilled instructor). It was a bit bittersweet to see his retirement announcement last year in the alumni newsletter; he certainly has earned a break but future Blue Hens will have to hope for a very able replacement.

It is my general contention that biology is very different from the other major sciences. My freshman-level physics class (which I couldn't schedule until my senior year) had a syllabus which essentially ended at the beginning of the 1900s. Again, this is no knock on the course or its wonderful professor; it's just that kinetics and electromagnetics on a macro scale was pretty much worked out by then. We had lots of supplementary material on more modern topics such as gravity assists from planets, fixing Hubble's mirror problem and quantum topics, but that was all gravy.

Similarly, my freshman chemistry course (again, quite good) covered science up to about World War II. My sophomore organic chemistry course pushed a little further in the century. It's not that these are backwards fields but quite the opposite -- enough had been learned by those time points to fill two semesters of introductory material.

But, I can't say the same about biology. In the two decades and change since my freshman biology coursework, I can certainly think of major discoveries either made or cemented in that time which deserve the attention of the earliest students. Like the course I assisted with at Harvard, my course had one semester of cells and smaller biology and one of organisms and bigger; I'll mostly focus on the cells and smaller because that's where I spend most of my time. But, there are certainly some strong candidates for inclusion in that other course. I'll also recognize the fact that perhaps for space reasons some of these topics would necessarily be pushed into the second tier courses which specialize in an area such as genetics or cell biology.

One significant problem I'll punt on: what to trim down. I don't remember much fat in my course (indeed, beyond the membrane we didn't speak much at all on it that year!). Perhaps that's what I have forgotten, but I think it more likely it was already pretty packed. I can think of some problem set items that can be jettisoned (Maxam-Gilbert sequencing is a historical curiosity at this point; I can think of much more relevant procedures to do on paper).

One topic I've convinced myself belongs in the early treatment is the proteasome, and not because I once spent a lot of time thinking about it (and also saw some financial gain -- though I no longer have such an interest in it). This is definitely a field which didn't exist on solid ground when I went through school, so it's absence from my early education First, it fits neatly into one of the key themes of introductory biology: homeostasis. Cells and organisms have mechanism for returning to a central tendency, and the proteasome plays a role for proteins. Proteasomes also form a nice bookend with ribosomes -- we learned that proteins are born but not how they die. Furthermore, not only do proteins have a lifespan, but not every protein has the same lifespan -- and lifespans are not fixed at birth. Finally, another great learning in freshman bio is around enzyme inhibitor types -- and the proteasome is the ultimate enzyme inhibitor. Plus, I'd try to mention the case of "the enemy of my enemy protein is my friend" -- proteasomes can activate one protein by destroying its inhibitor.

That's also a nice segue into another major there worth developing: regulation. I think the main message here is that any time a cell needs to process an mRNA or protein, it's an opportunity for regulation. Post-translational modifications of proteins play a key role here.

Furthermore, it's worth noting that regulation often uses chains of proteins ("pathways"). These chains offer both new opportunities for regulation and signal amplification. We spent a lot of time looking at the chains of enzymes that turn sugars into energy. Of nearly equal importance is the idea that chains of proteins (and not all of them enzymes) can control a cell. In addition, it is important to recognize that these pathways are organized into functional modules, reflecting both opportunities for control and their evolution.

Clearly in this spot the fact that we can now sequence entire genomes deserves mention. Beyond that, I think the most important fact to impress on young minds is how bewildered we still are by even the simplest genomes.

Stem cells are an important concept, and not only because they are a hot topic in the popular press and political arena. This is a key idea -- cell divisions which proceed in an asymmetric pattern.

One final clear concept for inclusion at this level is epigenetics. It is key to underline that there are means to transmit information in a heritable way which are not specifically encoded in the DNA sequence -- as important as that sequence is.

I'm sure I've missed a bunch of topics. There are a lot of ideas in the grey zone -- I haven't quite convinced myself they belong in freshman bio but certainly belong a course up. For example, the fact that organisms can borrow from other genomes (horizontal transfer) or even permanently capture entire organisms (endosymbionts) certainly belongs in cell bio or genetics, but I'm not sure it quite fits freshman year (but nor am I certain it doesn't). Lipid rafts and primary cilia and all sorts of other newly discovered (or re-discovered) subcellular structures definitely would fit in my curriculum there. Gaseous signalling molecules would definitely warrant mention, though perhaps along with the hormones in the organisms and bigger semester.

With luck, many will read this and be kind enough (and kind while doing it) to point out the big advances of the last score of years which deserve inclusion as well -- and I also have little doubt that many freshman this year are being exposed to many topics I wasn't because exist they didn't.

3 comments:

For example, the fact that organisms can borrow from other genomes (horizontal transfer) or even permanently capture entire organisms (endosymbionts) certainly belongs in cell bio or genetics, but I'm not sure it quite fits freshman year (but nor am I certain it doesn't)

I would say that it does. At least at a simple level (sort of like epigenetics.) Otherwise the intern will get fixed in his/her mind that there is a 'tree' of life instead of what more appears to be a 'web' of life. 2nd gen sequencing is giving us better insight into how much gene transfer can occur.

Follow by Email

Search This Blog

About Me

Dr. Robison spent 10 years at Millennium Pharmaceuticals working with various genomics & proteomics technologies & working on multiple teams attempting to apply these throughout the drug discovery process. He spent 2 years at Codon Devices working on a variety of protein & metabolic engineering projects as well as monitoring a high-throughput gene synthesis facility. After a brief bit of consulting, he rejoined the cancer drug discovery field at Infinity Pharmaceuticals in May 2009. In September 2011 he joined Warp Drive Bio, a startup applying genomics to natural product drug discovery. Other recurring characters in this blog are his loyal Shih Tzu Amanda and his teenaged son alias TNG (The Next Generation).
Dr. Robison can be reached via his Gmail account, keith.e.robison@gmail.com
You can also follow him on Twitter as @OmicsOmicsBlog.